Coexpression cluster:C468

Full id: C468_Neutrophils_Eosinophils_cerebellum_occipital_Whole_temporal_parietal

Phase1 CAGE Peaks

Hg19::chr11:74459876..74459930,+	p1@RNF169
Hg19::chr12:76953574..76953598,-	p3@OSBPL8
Hg19::chr14:52327421..52327458,+	p3@GNG2
Hg19::chr17:11924129..11924200,+	p1@MAP2K4
Hg19::chr17:47439568..47439641,-	p2@ZNF652
Hg19::chr1:89149914..89149995,+	p1@PKN2
Hg19::chr20:60813535..60813592,+	p2@OSBPL2
Hg19::chr2:139259324..139259389,+	p1@SPOPL
Hg19::chr2:160472952..160473077,-	p1@BAZ2B
Hg19::chr2:201936328..201936416,-	p1@FAM126B
Hg19::chr2:24714108..24714152,+	p@chr2:24714108..24714152 +
Hg19::chr2:86850949..86851023,-	p1@RNF103
Hg19::chr3:184529948..184529990,+	p1@VPS8
Hg19::chr4:6784401..6784510,+	p1@KIAA0232
Hg19::chr4:89513578..89513670,+	p1@HERC3
Hg19::chr5:112043186..112043225,+	p2@APC
Hg19::chr6:137113489..137113569,-	p1@MAP3K5
Hg19::chr6:42531690..42531718,+	p2@UBR2
Hg19::chr7:30634347..30634400,-	p1@uc003tbj.2 p1@uc003tbl.3 p1@uc010kvv.2
Hg19::chr8:52811714..52811731,-	p3@PCMTD1
Hg19::chrX:80065146..80065250,-	p1@BRWD3

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0006464	protein modification process	0.0195237347183443
GO:0043412	biopolymer modification	0.0195237347183443
GO:0051983	regulation of chromosome segregation	0.0195237347183443
GO:0051988	regulation of attachment of spindle microtubules to kinetochore	0.0195237347183443
GO:0008608	attachment of spindle microtubules to kinetochore	0.0195237347183443
GO:0007254	JNK cascade	0.0195237347183443
GO:0031098	stress-activated protein kinase signaling pathway	0.0195237347183443
GO:0043687	post-translational protein modification	0.0216695468435289

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
leukocyte	1.99e-28	136
hematopoietic stem cell	1.08e-23	168
angioblastic mesenchymal cell	1.08e-23	168
hematopoietic lineage restricted progenitor cell	3.94e-23	120
myeloid leukocyte	1.18e-22	72
hematopoietic oligopotent progenitor cell	9.51e-22	161
hematopoietic multipotent progenitor cell	9.51e-22	161
nongranular leukocyte	4.08e-21	115
granulocyte monocyte progenitor cell	1.61e-19	67
hematopoietic cell	1.68e-19	177
myeloid lineage restricted progenitor cell	6.12e-19	66
macrophage dendritic cell progenitor	2.42e-17	61
myeloid cell	4.06e-17	108
common myeloid progenitor	4.06e-17	108
monopoietic cell	9.35e-17	59
monocyte	9.35e-17	59
monoblast	9.35e-17	59
promonocyte	9.35e-17	59
defensive cell	1.95e-16	48
phagocyte	1.95e-16	48
classical monocyte	4.27e-16	42
CD14-positive, CD16-negative classical monocyte	4.27e-16	42
mature alpha-beta T cell	9.26e-07	18
alpha-beta T cell	9.26e-07	18
immature T cell	9.26e-07	18
mature T cell	9.26e-07	18
immature alpha-beta T cell	9.26e-07	18

Uber Anatomy

Ontology term	p-value	n
adult organism	1.58e-44	114
neural tube	1.13e-24	56
neural rod	1.13e-24	56
future spinal cord	1.13e-24	56
neural keel	1.13e-24	56
regional part of nervous system	3.41e-23	53
regional part of brain	3.41e-23	53
regional part of forebrain	3.36e-22	41
forebrain	3.36e-22	41
anterior neural tube	3.36e-22	41
future forebrain	3.36e-22	41
central nervous system	1.17e-20	81
hematopoietic system	1.49e-20	98
blood island	1.49e-20	98
brain	5.19e-20	68
future brain	5.19e-20	68
nervous system	1.18e-19	89
telencephalon	1.51e-18	34
brain grey matter	2.19e-18	34
gray matter	2.19e-18	34
cerebral hemisphere	1.90e-17	32
hemolymphoid system	1.97e-17	108
regional part of telencephalon	2.31e-17	32
bone marrow	7.23e-15	76
regional part of cerebral cortex	1.07e-14	22
neocortex	1.81e-13	20
bone element	1.93e-13	82
cerebral cortex	1.94e-13	25
pallium	1.94e-13	25
neurectoderm	2.99e-13	86
neural plate	3.40e-13	82
presumptive neural plate	3.40e-13	82
immune system	5.18e-13	93
skeletal element	4.64e-11	90
skeletal system	1.47e-10	100
pre-chordal neural plate	1.51e-10	61
ecto-epithelium	1.27e-07	104
ectoderm-derived structure	5.06e-07	171
ectoderm	5.06e-07	171
presumptive ectoderm	5.06e-07	171

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	6	6.41804986457393	0.000236156037347543	0.00257317687892958
BCLAF1#9774	6	6.1864707457491	0.000288025733388233	0.00306137996838323
BHLHE40#8553	3	6.41025907813963	0.0108955713046206	0.0401752072971074
BRCA1#672	5	4.80576920076756	0.00311220770626331	0.0163605909616165
CCNT2#905	13	3.92241050002449	2.16439215182906e-06	7.82711052440703e-05
CHD2#1106	8	3.94058012728261	0.000486716808846778	0.0043528187017596
CTCF#10664	12	3.06300364175716	9.61865604962896e-05	0.00136973386851268
CTCFL#140690	6	5.64184981684982	0.00047207889284908	0.00433360705724401
E2F1#1869	13	3.03790760921101	3.99747315883528e-05	0.000733987516236986
E2F4#1874	7	4.22268677176148	0.000821488692701318	0.00625696160859342
E2F6#1876	12	2.86694613239851	0.000187355136866969	0.0022655069050885
EGR1#1958	15	3.56298506772153	5.29066604052795e-07	2.46895384542761e-05
ELF1#1997	19	3.85256481987349	1.40187937768485e-10	1.49094582816729e-08
ELK4#2005	5	3.86563849011143	0.00784174642244141	0.0322054327413826
GABPB1#2553	12	4.03867647781838	5.38690292930369e-06	0.000164551844116276
GTF2F1#2962	6	3.63990310764504	0.0045165025117295	0.0213535086384118
HDAC2#3066	6	3.83303435332179	0.00349248373986806	0.0177373813123945
HEY1#23462	18	3.46295232266204	7.24417577880214e-09	5.62508902722912e-07
HMGN3#9324	11	4.28400118842174	9.84651420879756e-06	0.000258252159079008
IRF1#3659	15	5.45511696683136	1.40708023377392e-09	1.26032635107302e-07
IRF3#3661	3	6.71170745878423	0.00962080919135682	0.0362059560080756
JUND#3727	10	3.33079235327192	0.000274749498267518	0.00292891322339097
MAX#4149	11	3.37991002852754	9.5149658187134e-05	0.00136221180965128
MXI1#4601	8	3.79488443000354	0.000628244508876776	0.00516965240014037
MYC#4609	13	3.23284115861534	1.98900354493168e-05	0.00044160191587823
NFKB1#4790	12	3.13603624239648	7.56729836316575e-05	0.00117101951955944
PAX5#5079	11	3.49358194490267	6.97253825644776e-05	0.00110535052059069
POLR2A#5430	21	2.14745317655807	1.06914340939766e-07	6.24149069502978e-06
POU2F2#5452	10	4.33624955130596	2.84162272309111e-05	0.000599184808352337
RFX5#5993	6	3.44226023634146	0.00594226718672113	0.0266502530473641
SIN3A#25942	13	3.34835721183794	1.33646012272453e-05	0.000326194341568654
SP1#6667	13	3.52756942456341	7.37205723419176e-06	0.000211577434867203
SRF#6722	8	5.25606790939726	6.54168363195151e-05	0.00106153961596859
TAF1#6872	20	3.18385360547171	4.92884944828003e-10	4.77961102626664e-08
TAF7#6879	8	4.35545501139959	0.000244884603601936	0.00266328263205067
TBP#6908	19	3.35374490737292	1.79157243688477e-09	1.55665585470723e-07
TFAP2A#7020	5	3.93300818405832	0.00729722465606885	0.0301851570760129
TFAP2C#7022	6	3.08835103138864	0.0100203796174012	0.0375702181605372
USF1#7391	8	2.42342829607922	0.0110256795158652	0.04055901317169
YY1#7528	16	3.74184438084103	6.13111176653469e-08	3.79790736527353e-06
ZBTB7A#51341	9	3.15081827480396	0.000990362042529161	0.00710826894094585
ZEB1#6935	7	5.62947733918129	0.000141337696225697	0.00184238238343929
ZZZ3#26009	2	22.8012583271651	0.0034712349908987	0.0176320369249778

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.